While there are some compatibility issues, the latest mapper pack has resolved nearly all of them. Make sure you have the latest and also try flipping the DMA setting on/off, as it affects compatibility as well.
Also, RetroUSB has stated the NES PowerPak will not work on clone hardware. This is from their site.
Unlike the NES PowerPak, he SNES PowerPak will work on clone systems.System Compatibility List:
Works on authentic Nintendo Systems including NTSC, PAL A, PAL B, and Asian top loader and toaster systems.
Works on Famicom using 72-60 pin converter.
Does NOT work on clone systems like the NEX, Yobo, or FC Twin.
Untested on portable systems, not likely to work.